##Download gene annotation databases
system("perl annotate_variation.pl -downdb -buildver hg18 gene humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 knownGene humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 ensGene humandb/");
##Download region annotation databases from UCSC
system("perl annotate_variation.pl -downdb -buildver hg18 band humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 tfbs humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 mce28way humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 segdup humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 mirna humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 mirnatarget humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 evofold humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 dgv humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 omimgene humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 gwascatalog humandb/ ");
system("perl annotate_variation.pl -downdb -buildver hg18 phastConsElements28wayPlacMammal humandb/");
#Download 1000 Genome Project, dbSNP, SIFT, Polyphen, MutationTaster and other filter-based annotation databases
system("perl annotate_variation.pl -downdb 1000g2010 humandb/ ");
system("perl annotate_variation.pl -downdb -buildver hg18 snp130 humandb/");
system("perl annotate_variation.pl -downdb -buildver hg18 avsift humandb/");

system("perl annotate_variation.pl -downdb -buildver hg18 cytoBand humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb refgene humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb phastConsElements46way humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb genomicSuperDups humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb snp135 -webfrom annovar humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb avsift -webfrom annovar humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb ljb_all -webfrom annovar humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb esp6500_all -webfrom annovar humandb/");
system("perl annotate_variation.pl -buildver hg18 -downdb wgEncodeCaltechRnaSeqRawSignalRep1Gm12878CellLongpolyaBb12x75 humandb/");
